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Iron in PDB 3b3n: Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine

Enzymatic activity of Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine

All present enzymatic activity of Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine, PDB code: 3b3n was solved by J.Igarashi, H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.64 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.050, 110.690, 164.840, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27

Other elements in 3b3n:

The structure of Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine (pdb code 3b3n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine, PDB code: 3b3n:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3b3n

Go back to Iron Binding Sites List in 3b3n
Iron binding site 1 out of 2 in the Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe750

b:24.1
occ:1.00
 FE A:HEM750 0.0 24.1 1.0
NA A:HEM750 2.0 26.4 1.0
ND A:HEM750 2.0 25.0 1.0
NC A:HEM750 2.0 24.2 1.0
NB A:HEM750 2.0 27.7 1.0
SG A:CYS415 2.2 29.9 1.0
C4A A:HEM750 3.0 25.7 1.0
C1C A:HEM750 3.1 24.8 1.0
C1A A:HEM750 3.1 25.7 1.0
C4C A:HEM750 3.1 23.3 1.0
C4D A:HEM750 3.1 24.2 1.0
C1D A:HEM750 3.1 23.9 1.0
C1B A:HEM750 3.1 26.0 1.0
C4B A:HEM750 3.1 28.0 1.0
CB A:CYS415 3.3 27.5 1.0
CHD A:HEM750 3.4 24.0 1.0
CHC A:HEM750 3.4 26.6 1.0
CHA A:HEM750 3.4 23.9 1.0
CHB A:HEM750 3.5 25.2 1.0
C4 A:JI2800 4.1 25.8 1.0
CA A:CYS415 4.1 27.1 1.0
C5 A:JI2800 4.2 24.9 1.0
C3A A:HEM750 4.3 25.9 1.0
C3D A:HEM750 4.3 24.0 1.0
C2A A:HEM750 4.3 24.5 1.0
C2C A:HEM750 4.3 22.5 1.0
C3C A:HEM750 4.3 24.1 1.0
C2D A:HEM750 4.3 24.0 1.0
C2B A:HEM750 4.3 28.8 1.0
C3B A:HEM750 4.4 28.0 1.0
NE1 A:TRP409 4.4 22.9 1.0
C3 A:JI2800 4.4 26.0 1.0
C6 A:JI2800 4.6 26.2 1.0
C2 A:JI2800 4.8 26.6 1.0
C A:CYS415 4.9 26.5 1.0
N1 A:JI2800 4.9 27.7 1.0
N A:GLY417 4.9 25.3 1.0
N A:VAL416 5.0 25.0 1.0

Iron binding site 2 out of 2 in 3b3n

Go back to Iron Binding Sites List in 3b3n
Iron binding site 2 out of 2 in the Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Neuronal Nos Heme Domain in Complex with A Inhibitor (+-)-N1-{Cis-4'-[(6"-Aminopyridin-2"-Yl) Methyl]Pyrrolidin-3'-Yl}Ethane-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe750

b:23.1
occ:1.00
 FE B:HEM750 0.0 23.1 1.0
ND B:HEM750 2.0 23.7 1.0
NC B:HEM750 2.0 22.1 1.0
NA B:HEM750 2.0 24.7 1.0
NB B:HEM750 2.0 24.7 1.0
SG B:CYS415 2.3 25.6 1.0
C1D B:HEM750 3.0 21.9 1.0
C4C B:HEM750 3.0 22.0 1.0
C4D B:HEM750 3.0 24.6 1.0
C1A B:HEM750 3.0 24.4 1.0
C1C B:HEM750 3.1 21.9 1.0
C4B B:HEM750 3.1 24.9 1.0
C4A B:HEM750 3.1 23.7 1.0
C1B B:HEM750 3.1 23.9 1.0
CHD B:HEM750 3.4 23.3 1.0
CHA B:HEM750 3.4 24.5 1.0
CB B:CYS415 3.4 22.1 1.0
CHC B:HEM750 3.4 22.4 1.0
CHB B:HEM750 3.5 25.9 1.0
C4 B:JI2800 4.1 30.5 1.0
CA B:CYS415 4.2 22.5 1.0
C5 B:JI2800 4.2 25.9 1.0
C2D B:HEM750 4.2 22.6 1.0
C3C B:HEM750 4.3 21.8 1.0
C3D B:HEM750 4.3 23.9 1.0
C2A B:HEM750 4.3 23.2 1.0
C2C B:HEM750 4.3 22.0 1.0
C3A B:HEM750 4.3 23.1 1.0
C3B B:HEM750 4.3 26.1 1.0
NE1 B:TRP409 4.4 19.0 1.0
C2B B:HEM750 4.4 26.2 1.0
C3 B:JI2800 4.5 30.4 1.0
C6 B:JI2800 4.6 28.4 1.0
N B:GLY417 4.8 25.1 1.0
C2 B:JI2800 4.8 29.4 1.0
C B:CYS415 4.9 22.7 1.0
N1 B:JI2800 4.9 28.6 1.0
N B:VAL416 5.0 23.0 1.0
CD1 B:TRP409 5.0 20.5 1.0

Reference:

H.Ji, B.Z.Stanton, J.Igarashi, H.Li, P.Martasek, L.J.Roman, T.L.Poulos, R.B.Silverman. Minimal Pharmacophoric Elements and Fragment Hopping, An Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors. J.Am.Chem.Soc. V. 130 3900 2008.
ISSN: ISSN 0002-7863
PubMed: 18321097
DOI: 10.1021/JA0772041
Page generated: Sun Aug 4 07:35:23 2024

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